the function running() works fine. When the jquery animate() function stops, it moves on as expected, though without the "move" variable it doesn't. The setTimeout keeps firing even after I call the clearTimeout.

Anyway, it gets to startTurning() and does it's thing then starts the turning() function where it seems to return to startTurning(). What happens after a setTimeout finishes? Does it return to where it was triggered or continue from the function it triggered?

Any help is appreciated.

“Be ashamed to die until you have won some victory for humanity.” -- Horace Mann

First, it's good practice to give your variable appropriate scope using the var keyword. For example, at the top of your script declare var ti; so people know it is shared between those functions, and inside the running function declare var move; so that people know the variable belongs only to that function. Otherwise it's really hard to figure out which variables belong to which scope.

Second, I'm pretty sure this code will end up creating many timers because:
(1) running is called every 80 milliseconds
(2) running always creates a new timer unless move is 0
(3) move does not become 0 until after 2000 milliseconds

So when you do a clear on ti, you're only clearing the most recent timer. You've lost the reference to the others at that point, so can't clear them.

What happens after a setTimeout finishes? Does it return to where it was triggered or continue from the function it triggered?

No, neither, setTimeout is asynchronous. After it's done, it's just done. The code after your setTimeout call continues executing immediately after the initial call, before setTimeout has triggered at all.

I just realized you're using setTimeout instead of setInterval, so the problem with creating multiple timers is actually less of an issue than it would have been if you were using setInterval. However, it's more appropriate in a case like this to use setInterval rather than setTimeout anyway.

Tracking the animation state, like you're doing with move, is important.